RetrogeneDB ID: retro_dnov_2547

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8473:1212..1984(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: IDO1
• Ensembl ID: ENSDNOG00000002167
• Aliases: None
• Description: indoleamine 2,3-dioxygenase 1 [Source:HGNC Symbol;Acc:6059]

Sequence

>retro_dnov_2547
GACTAGGCATCTCCTATGGAAAGTTCTTTAAAAATCCATGAGGAATTCCACATAGATGAAGAGGTGGGCTTTGCTCTGCT
AAATCCACCGGAGTAGTTGCCTAATAAGTATGCTGCCTGGATATTCATTGCTCAAAATCTGCCTGACCTGATTATGATTA
GCCAGTTATGCACAGAAGCTGAAAAGTTGCCAGAGCTCAGCGTCGATGACCTCAAAGGATGCAAATTGCTGCACTTGACC
ACCTGATCTTGAAGTACATCATCATGGCCTATGTGTGGGATCAAGGTGACCAAGATGTCCACAAGGTCCTGCCAAGAAAT
ATTGCCATGCCATACTGCAAAATCTTGGAGAAGCTTAGACTGCCTTCTATTCTGGTTTACACAGATTGTGTCTTTGCAAA
CTGGGAGAAAAAGGATTCCAATGGACCCATGACTTATGAGAACATGGACATCCTGTTCTTCTTCCCTGGTGGAGACTACA
GAAAAGGTTTCTTCCCACTGTCACTAATTGTGGAAATAGCAGCTGCTTCTGTGATCAAAGAAATTCCCATATTCCATGCT
ATACAACACCAGGACCAGTGAACTATAAAAACAGAACTGGAAAAATTAACTGATTGCCTGAAGAAAGCCTTGGAAGTATT
TAGGCAAATTCACAAATACTTGGACCCAAAGGGATTTTTCAATGTTCTTTGCATCTTCTTGTCTGGCTGGAAAGGCAACT
CCCAGCTGCCAAAAGGCCTGCTGTATGAAAGGGTCTGGGAACCCCACAACAA

Alignment

ORF - retro_dnov_2547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.2 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DQASPMESPWRIREEFHINEDVGFALPDPLEELPKKYDDWMFIAQNLPDLIKTGKLREEVEKLPELSIDD
          D.ASPMES...I.EEFHI.E.VGFAL..P.E.LP.KY..W.FIAQNLPDLI....L..E.EKLPELS.DD
Retrocopy D*ASPMESSLKIHEEFHIDEEVGFALLNPPE*LPNKYAAWIFIAQNLPDLIMISQLCTEAEKLPELSVDD

Parental  LEGHKLQRLA-HLVLGYITMAYVWDRGDQDVRKVLPRNIAIPYCRISEMLKLPPILSYADCVLANWKKKD
          L.G.KL..L..HL.L.YI.MAYVWD.GDQDV.KVLPRNIA.PYC.I.E.L.LP.IL.Y.DCV.ANW.KKD
Retrocopy LKGCKLLHLT<HLILKYIIMAYVWDQGDQDVHKVLPRNIAMPYCKILEKLRLPSILVYTDCVFANWEKKD

Parental  PSG---VKNMEILFSFPGGDCGKGFFLVSLLVEIAAASVIKEIPILINAIQHQDQATVKTELEKITGCLK
          ..G.....NM.ILF.FPGGD..KGFF..SL.VEIAAASVIKEIPI...AIQHQDQ.T.KTELEK.T.CLK
Retrocopy SNGPMTYENMDILFFFPGGDYRKGFFPLSLIVEIAAASVIKEIPIF-HAIQHQDQ*TIKTELEKLTDCLK

Parental  EALEAFTQFHKYVDPNNFFNILRIYLSGWKNSSKLPEGLLYEGVWD-TPKQ
          .ALE.F.Q.HKY.DP..FFN.L.I.LSGWK..S.LP.GLLYE.VW..TP.Q
Retrocopy KALEVFRQIHKYLDPKGFFNVLCIFLSGWKGNSQLPKGLLYERVWE<TPQQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	3.50 RPM
SRP012922_cerebellum	0.00 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	10.44 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	1.08 RPM
SRP012922_lung	0.00 RPM	411.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.58 RPM
SRP012922_spleen	0.00 RPM	29.42 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2547 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002167	3 retrocopies	retro_dnov_1689, retro_dnov_2547 , retro_dnov_2609,